Global metadata effective population size analysis

we want to describe large clades that differ in some metadata with respect to the rest of the tree. First we look at the distribution of mosaic variants of the genes mtr and penA, minimum inhibitory concentration (MIC) (categorised into levels high and low) levels, and sex distribution,

Tree with metadata

The fully annotated tree shows that most of the mosaic variant of mtr clusters in distict part of the tree. High HIC categories also clusters in some sections of the tree. The sex distribution does not have major evident clusters when we look at the tree as a whole, but in smaller sections of the tree.

An interactive version of the plot can be explored below

Clades

The pictures below shows subtrees (see interactive plot) we deem important and for which we will estimate the effective population size dynamics.

MTR clusters in the upper part of the tree under node 11506. The estimated time of the most recent common ancestor (TMRCA) of this clade is around 1978.

The PenA MIC values make up three distict clusters. The first picture shows a clade with an estimated high MIC that carries a mosaic penA gene variant. The estimated tmrca of this clade around 1959.The second clade´s tmrca is around 1976, and has the same MIC and penA mosaic profile, but includes a sub-group with different form of mosaic pen-A (denoted semi-mosaic in the figure in dark blue) The third clade´s tmrca is approximately 1940 show a clade with high MIC, but non-mosaic penA profile.

Population dynamcis in the clades

TBD

All of the clades grew in the period 1980-2010. After 2010 the effective population size falls for all the clades define by penA variants, while mtr continues growing or alternatively stablizes. The effective population size in the tree as a whole is shown below. The clades from above are highlighted.

The high effective population size from 1770-1800 is a result of the long basal branches which probably displays a lack of sequences that represent the divergence that happened in this time period. From 1810-2010 the effective population size have been steadily growing, with a pronounced decrease since 2010.